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- PDB-5n13: Second Bromodomain (BD2) from Candida albicans Bdf1 in the unboun... -

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Basic information

Entry
Database: PDB / ID: 5n13
TitleSecond Bromodomain (BD2) from Candida albicans Bdf1 in the unbound form
ComponentsBromodomain-containing factor 1
KeywordsTRANSCRIPTION / Bromodomain
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / histone binding / DNA repair / nucleus
Similarity search - Function
NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing factor 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMietton, F. / Ferri, E. / Champlebouxm, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. ...Mietton, F. / Ferri, E. / Champlebouxm, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. / Cornet, M. / McKenna, C.E. / Govin, J. / Petosa, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE16-0027-01 France
CitationJournal: Nat Commun / Year: 2017
Title: Selective BET bromodomain inhibition as an antifungal therapeutic strategy.
Authors: Mietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. ...Authors: Mietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. / Cornet, M. / McKenna, C.E. / Govin, J. / Petosa, C.
History
DepositionFeb 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8113
Polymers12,6261
Non-polymers1842
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-1 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.754, 45.196, 71.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing factor 1


Mass: 12626.337 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: BDF1, CaO19.8593, CaO19.978 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5A4W8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M TRIS-HCl (pH 8.5) and 1 M ammonium phosphate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.2→45.2 Å / Num. obs: 39415 / % possible obs: 97.9 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Net I/σ(I): 17
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3 / Num. unique obs: 3330 / CC1/2: 0.918 / Rpim(I) all: 0.18 / % possible all: 83.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUO

2ouo


Resolution: 1.2→38.253 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.31
RfactorNum. reflection% reflectionSelection details
Rfree0.156 1980 5.03 %Random selection
Rwork0.1426 ---
obs0.1432 39353 97.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 1.2→38.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 12 194 1083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004907
X-RAY DIFFRACTIONf_angle_d0.7631222
X-RAY DIFFRACTIONf_dihedral_angle_d11.71339
X-RAY DIFFRACTIONf_chiral_restr0.073128
X-RAY DIFFRACTIONf_plane_restr0.006160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.22861090.17372204X-RAY DIFFRACTION82
1.23-1.26330.18221270.1452467X-RAY DIFFRACTION91
1.2633-1.30050.14081260.13812628X-RAY DIFFRACTION98
1.3005-1.34240.15031370.12152683X-RAY DIFFRACTION100
1.3424-1.39040.16451610.11882683X-RAY DIFFRACTION100
1.3904-1.44610.12521550.1162666X-RAY DIFFRACTION100
1.4461-1.51190.14411300.10522727X-RAY DIFFRACTION100
1.5119-1.59160.13941230.10422701X-RAY DIFFRACTION100
1.5916-1.69130.11971590.10572727X-RAY DIFFRACTION100
1.6913-1.82190.13661470.12252715X-RAY DIFFRACTION100
1.8219-2.00530.14121670.13272690X-RAY DIFFRACTION100
2.0053-2.29540.16011340.13382791X-RAY DIFFRACTION100
2.2954-2.89180.17171430.16032781X-RAY DIFFRACTION100
2.8918-38.27250.16761620.172910X-RAY DIFFRACTION100

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